Genomic
islands can be
located due to their divergent tetranucleotide usage compare to the
core genome. A key feature of the SeqWord Genome Browser is the use of
three distinct parameters to identify genomic islands, instead of
simply the traditional GC alteration.

To
select all genomic islands of a
bacterial genome, go to the tab ‘Diagram’.

Select
n1_4mer:RV for the X axis,
n1_4mer:GRV for the Y axis and n0_4mer:D for
the
Z axis.

Click
the button ‘Enter’.

Genomic
fragments that
correspond to putatively horizontally transferred elements are
presented in a cloud of
green, brown or red dots above the lower part of the mainstream
diagonal
distribution of the core genome fragments. Select the dots as shown on
the image and click the button ‘Get’.

The
above image is of
Pseudomonas putida
KT2440, which as a known mosaic genome contains many
genomic fragments dissimilar to the genomic average.

For
more precise identification
use the filter with the sliders set as shown:

Warning
- the vertical layout
of the parameters may change according to how many parameters are
calculated
for the sequence.

Having set
the filter, only
fragments that correspond to gene islands remain on the dot-plot:

This
method has been successfully demonstrated for several strains
with known genomic islands:

- the large 680kb symbiotic island in Bradyrhizobium
japonicum USDA110

All
above mentioned genomic islands were successfully localized following
comparison of local and global OU patterns.

However,
not all islands are quite so divergent. For example, some islands may
have been gained from a location compositionally similar to the current
genome (for example, from a strain with similar GC content and
tetranucleotide usage). These islands are thus more difficult to detect.

For
example, Mesorhizobium loti
MAFF303099 contains a large symbiotic island (similarly to B. japonicum
USDA110).
The island has an average GC content of 59.4 % compared to the genomic
average of 64 %, and as such may have been partially ameliorated (where
the island GC and OU patterns become more similar to the host OU over
time due to accumulations of mutations in especially redundant codon
positions. Whether ameriolation has taken place or not, this island is
difficult to detect with the current protocol. The below
screenshot shows a dotplot of this strain. Fragments within the island
coordinates (here 4.70MB to 5.20MB) have been coloured yellow with the "Mark" button, and are
not distinct enough from the core genome (coloured blue) to
be reliably detected.

Vibrio cholerae
N16961-O1-eltor possesses two chromosomes, the second
and smaller of which (at 1.07MB) has a large abnormal region termed the
integron island, which has been suggested to function as a gene capture
system. We initially attempted to find the island visually using the
"Gene Map" tab. As this is such a divergent feature in all parameters,
it is clearly visible just left of centre in the figure below.

Next we plotted the genomic fragments in the "Diagram" tab (below).
This chromosome provides a distinctly different image to the
Pseudomonas putida KT2440 used in the aforementioned
protocol, with
more aberrant regions with high divergence occurring across the range
of RV values. The P. putida values were more densely clustered in the
genomic core and coloured blue, indicating a low Distance of the
fragment from the genomic norm. Here with V. cholerae, we see many more
fragments distinct from the core genome (coloured green).

Can we then find all genomic fragments which are part of
the 0.125MB
large integron island using the filtering protocol ? Only three of the
filtered fragments were in the island. This is only a small portion of
those which should be present (125kb / 8 kb fragments = 15 fragments).

The island has a GC content considerably below the chromosomal average
of 47%. Average pattern skew (which is typically low for chromosomes
but higher in plasmids and phages) is relatively high at 32%. It
seems that either a) this island is large enough (making up 0.125MB
of the 1.07MB chromosome (Heidelberg et al 2000) to influence
chromosome wide parameters or b) the chromosome as a whole is in a
state of instability or flux according to our parameters.

So is V. cholerae chromosome I any different ?

In short, yes. V. cholerae chromosome I is more similar to that of
P.
putida KT2440 discussed previously, with a well defined core (blue)
with little scatter of highly distant genomic fragments around it (see
below).

Concluding remarks

The SeqWord genome browser effectively locates divergent fragments of
most genomic islands in most chromosomes using several parameters and
two distinct perspectives. Care must be taken when using this analysis
on chromosomes considered to be variable or in flux. These chromosomes
typically display a large degree of scattering of divergent fragments
(coloured green) around the (blue) genomic core.